title: Aptamers that recognize drug-resistant HIV-1 reverse transcriptase.
abstract: Drug-resistant variants of HIV-1 reverse transcriptase (RT) are also known to be resistant to anti-RT RNA aptamers. In order to be able to develop diagnostics and therapies that can focus on otherwise drug-resistant viruses, we have isolated two aptamers against a well-known, drug-resistant HIV-1 RT, Mutant 3 (M3) from the multidrug-resistant HIV-1 RT panel. One aptamer, M302, bound M3 but showed no significant affinity for wild-type (WT) HIV-1 RT, while another aptamer, 12.01, bound to both M3 and WT HIV-1 RTs. In contrast to all previously selected anti-RT aptamers, neither of these aptamers showed observable inhibition of either polymerase or RNase H activities. Aptamers M302 and 12.01 competed with one another for binding to M3, but they did not compete with a pseudoknot aptamer for binding to the template/primer cleft of WT HIV-1 RT. These results represent the surprising identification of an additional RNA-binding epitope on the surface of HIV-1 RT. M3 and WT HIV-1 RTs could be distinguished using an aptamer-based microarray. By probing protein conformation as a correlate to drug resistance we introduce an additional and useful measure for determining HIV-1 drug resistance.
authors.affiliation: Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
authors.forename: Na
authors.initials: N
authors.lastname: Li
authors.forename: Yuxuan
authors.initials: Y
authors.lastname: Wang
authors.forename: Arti
authors.initials: A
authors.lastname: Pothukuchy
authors.forename: Angel
authors.initials: A
authors.lastname: Syrett
authors.forename: Naeem
authors.initials: N
authors.lastname: Husain
authors.forename: Siddharth
authors.initials: S
authors.lastname: Gopalakrisha
authors.forename: Pradeepa
authors.initials: P
authors.lastname: Kosaraju
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Ellington
mesh_terms: D019380:Anti-HIV Agents / Q000627:therapeutic use; D052157:Aptamers, Nucleotide / Q000737:chemistry*; D001483:Base Sequence; D024882:Drug Resistance, Viral / Q000235:genetics*; D054303:HIV Reverse Transcriptase / Q000032:analysis* / Q000737:chemistry / Q000235:genetics; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D040081:Protein Array Analysis
chemical_list: D019380:Anti-HIV Agents; D052157:Aptamers, Nucleotide; C514824:reverse transcriptase, Human immunodeficiency virus 1; D054303:HIV Reverse Transcriptase